The Emergence of HIV: A Molecular Archeology Approach

因为像HIV-1这样的逆转录病毒进化得如此之快，从出现之前的短短几十年中检索到的病毒基因序列实际上是分子“化石”。这样的化石序列可以用来提供无可争议的证据，证明特定微生物在早期的时间点存在，并验证否则无法测试的历史推断。它们照亮了原本会丢失的遥远过去的部分，并为我们提供了测试关于医学上重要病毒的起源和进化轨迹的至关重要的假设的手段。尽管控制艾滋病毒的战斗始终需要对其目前的遗传多样性有最好的了解，但这种理解只能通过在历史遗传变异的背景下查看当代基因序列来实现。只有几个值得注意的 例外情况“分子考古学”的观点到目前为止还没有被用于艾滋病毒-1 M组，这是本提案的重点。该项目的总体目标是通过恢复和分析从过去收集的信息，全面和综合地努力了解艾滋病毒-1 M组的未来。为了做到这一点，我们将1.使用档案标本来揭示艾滋病毒在北美出现的历史，以确定海地是否是艾滋病毒-1 M亚型B亚型在发达国家蔓延之前的“垫脚石”；以及2.通过优化DMA提取方案，确定高灵敏度的PCR筛选引物，在前所未有的早期时间点调查艾滋病毒-1在中部非洲的演变， 探索汇集样本的方法，并筛选我们存档的非洲组织样本的一小部分。至关重要的是，我们收集了大量的档案材料，其中许多来自艾滋病毒研究领域尚未被广泛考虑的来源，我们将用这些材料来阐明艾滋病毒进化的显著未被研究的早期阶段(大约从发现艾滋病的时间，追溯到1955年，甚至更早)。

Because retroviruses like HIV-1 evolve so rapidly, viral genetic sequences retrieved from just a few decades before present are effectively molecular 'fossils'. Such fossil sequences can be used to provide indisputable evidence of the existence of a given microbe at an early time point, and to validate historical inferences that could otherwise not be tested. They light up portions of the deep past that would otherwise be lost, and give us the means to test critically important hypotheses about the origins and evolutionary trajectories of medically important viruses. Although the battle to control HIV will always require the best possible understanding of its current genetic diversity, such understanding can only be achieved by viewing contemporary gene sequences in the context of historical genetic variation. With just a handful of notable exceptions the 'molecular archeology' perspective has to date not been exploited with respect to HIV-1 group M, the focus of this proposal. The overarching aim of this project is to make a comprehensive and integrated effort to understand the future of HIV-1 group M by recovering then analyzing information gleaned from its past. To do this we will 1. use archival specimens to uncover the history of the emergence of HIV in North America to determine whether Haiti was the "stepping stone" of HIV-1 group M subtype B before it spread around the developed world; and 2. investigate the evolution of HIV-1 in central Africa at an unprecedented early time point by optimizing DMA extraction protocols, identifying high-sensitivity PCR screening primers, exploring methods for pooling samples, and screening a small subset of our archived African tissue specimens. Crucially, we have assembled a massive collection of archival materials, many from sources that have not yet been widely considered in the field of HIV research, with which we will illuminate the remarkably unstudied early phase of HIV evolution (from around the time of the discovery of AIDS, back to 1955 and perhaps even earlier).